AMBER Archive (2006)

Subject: Re: AMBER: pmemd_parallel_ins_prob

From: pkmukher (pkmukher_at_olemiss.edu)
Date: Thu Jun 08 2006 - 13:09:00 CDT

Robert

    Thanks for your advice.I will try to get the latest
fortran compiler from sgi.Could you also guide me as to how
i should lower the optimization level of the file.I am a
novice at these things.Many thanks

> Prasenjit,
> It is a compiler bug, one I have not seen however. Can
> you get an updated version of the compiler from sgi? If
> not, you might consider lowering the optimization level
> for the file that the compiler is processing when it
> crashes, but I suspect this will not help because the
> indication is that the compiler cannot parse the file (in
> other words, it was not generating code when it failed).
> I would probably also check for repeatability, to insure
> it is not hardware issues. Regards - Bob Duke
>
> ----- Original Message -----
> From: "pkmukher" <pkmukher_at_olemiss.edu>
> To: <amber_at_scripps.edu>
> Sent: Wednesday, June 07, 2006 5:00 PM
> Subject: AMBER: pmemd_parallel_ins_prob
>
>
> > Hi,
> >
> > I am getting the following error message when
> > installing the pmemd module in the parallel
> > implementation.It is said that the autoconfiguration
> > scripst might be causing these problems.If that is the
> > case could you suggest how i need to modify my
> > configuration file to get the desired results.The
> terminal output is given below.I have also added the
> > output from the hinv command.
> >
> > Thanking you in anticipation
> >
> >
> >
> > uranium 7% ./configure sgi_mips f90 mpi
> > PMEMD Configurate successfully completed.
> > uranium 8% make install
> > cd src; make install
> > ../Compile OPT_HI -P gbl_constants.f90
> > cat gbl_constants.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _gbl_constan
> > ts_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
> > it_intrinsics=ON _gbl_constants_.f90
> > ../Compile OPT_HI -P gbl_datatypes.f90
> > cat gbl_datatypes.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _gbl_datatyp
> > es_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
> > it_intrinsics=ON _gbl_datatypes_.f90
> > ../Compile OPT_HI -P file_io_dat.f90
> > cat file_io_dat.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _file_io_dat_.
> > f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
> > it_intrinsics=ON _file_io_dat_.f90
> > touch use_gbl_datatypes.h
> > ../Compile OPT_HI -P parallel_dat.f90
> > cat parallel_dat.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _parallel_dat
> > _.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
> > it_intrinsics=ON _parallel_dat_.f90
> > ../Compile OPT_MED -P file_io.f90
> > cat file_io.f90 | /lib/cpp -P -DMPI -DDIRFRC_VECT_OPT
> > -DSGIFFT > _file_io_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_b
> > it_intrinsics=ON _file_io_.f90
> > touch use_file_io.h
> > touch use_gbl_constants.h
> > touch use_parallel_dat.h
> > ../Compile OPT_HI -P mdin_ctrl_dat.f90
> > cat mdin_ctrl_dat.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _mdin_ctrl_dat_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
> > _mdin_ctrl_dat_.f90
> > ../Compile OPT_HI -P axis_optimize_cit.f90
> > cat axis_optimize_cit.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _axis_optimize_cit_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
> > _axis_optimize_cit_.f90
> > touch use_axis_optimize_cit.h
> > touch use_mdin_ctrl_dat.h
> > ../Compile OPT_HI -P mdin_ewald_dat.f90
> > cat mdin_ewald_dat.f90 | /lib/cpp -P -DMPI
> > -DDIRFRC_VECT_OPT -DSGIFFT > _mdin_ewald_dat_.f90
> > f90 -nocpp -r16000 -mips4 -n32 -c -O3 -old_rl
> > -OPT:roundoff=3:IEEE_arithmetic=3:fast_bit_intrinsics=ON
> > _mdin_ewald_dat_.f90
> > Signal: Bus error in Front End Parse/Semantic phase.
> > Error: Signal Bus error in phase Front End
> > Parse/Semantic -- processing aborted
> > f90 ERROR: /usr/lib32/cmplrs/mfef90 died due to signal
> > 4 f90 ERROR: core dumped
> > *** Error code 1 (bu21)
> > *** Error code 1 (bu21)
> >
> > uranium 1% hinv
> > 8 700 MHZ IP35 Processors
> > CPU: MIPS R16000 Processor Chip Revision: 2.1
> > FPU: MIPS R16010 Floating Point Chip Revision: 2.1
> > Main memory size: 2048 Mbytes
> > Instruction cache size: 32 Kbytes
> > Data cache size: 32 Kbytes
> > Secondary unified instruction/data cache size: 4 Mbytes
> > Integral SCSI controller 2: Version IDE (ATA/ATAPI) IOC4
> > Integral SCSI controller 0: Version QL12160, low voltage
> > differential
> > Disk drive: unit 1 on SCSI controller 0
> > Disk drive: unit 2 on SCSI controller 0
> > Integral SCSI controller 1: Version QL12160, single
> > ended Disk drive: unit 1 on SCSI controller 1
> > Disk drive: unit 2 on SCSI controller 1
> > Disk drive: unit 3 on SCSI controller 1
> > Disk drive: unit 5 on SCSI controller 1
> > CDROM: unit 6 on SCSI controller 1
> > IOC3/IOC4 serial port: tty3
> > IOC3/IOC4 serial port: tty4
> > IOC3/IOC4 serial port: tty5
> > IOC3/IOC4 serial port: tty6
> > Gigabit Ethernet: tg0, module 001c01, PCI bus 1 slot 4
> > IOC3/IOC4 external interrupts: 1
> >
> >
> >
> >
> > Prasenjit Kumar Mukherjee
> > Graduate Student
> > Department of Medicinal Chemistry
> > School of Pharmacy
> > University of Mississippi
> > USA
> >
> > Cell - 662 380 0146
> > Office - 662 915 1286
> >
> >
> >
> >
> >
> >
> >
> >
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>
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Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell - 662 380 0146
Office - 662 915 1286

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